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Sample GSM3108731 Query DataSets for GSM3108731
Status Public on Apr 23, 2021
Title Mock
Sample type SRA
 
Source name Bladder cancer cells
Organism Homo sapiens
Characteristics cell line: 5637 cells
chip antibody: 5-Methylcytosine (5-mC) Rabbit mAb (Cell Signaling 28692S)
agent: Mock
Treatment protocol 5637 cells were treated with 100nM DEC or with DEC and cisplatin combined daily for 72 hours
Growth protocol 10% FBS in DMEM
Extracted molecule genomic DNA
Extraction protocol 10–50 mg of genomic DNA for each sample was sonicated and used for the ligation of barcoded Illumina adapters. A total of 5 mg adaptor ligated DNA was used for immunoprecipitation by 5-Methylcytosine (5-mC) Rabbit mAb (Cell Signaling 28692S).
Sequencing libraries were generated using a DNA SMART ChIP-Seq Kit (Clonetech 634865) and pooling immunoprecipitated DNA from 3 independent samples.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 3000
 
Data processing Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 1.2.0.
The unique mapped reads was used for peak calling by MACS2 with default setting
Supplementary_files_format_and_content: wig file
 
Submission date Apr 23, 2018
Last update date Apr 23, 2021
Contact name Jiong Li
E-mail(s) jiongli@ucla.edu
Phone 3105617186
Organization name UCLA
Department School of Dentistry
Lab Cunyu Wang
Street address 33-030 CHS
City Los Angeles
State/province CA - California
ZIP/Postal code 91406
Country USA
 
Platform ID GPL21290
Series (1)
GSE113537 Genome-wide DNA methylation maps of Decitabine and/or Cisplatin treated bladder cancer cells.
Relations
BioSample SAMN08971279
SRA SRX3988556

Supplementary file Size Download File type/resource
GSM3108731_Mock.bw 194.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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